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How To Blast Kegg-Only Data In The 'Nr' Database

Hi there,

I dont have a locally KEGG database bought,but I want to Blast my sequences against only the KEGG part of nr db cause you know blast whole nr is really time consuming.

Here is my approach:

  1. download the KO number of a specific pathway that I'm interested in from the KEGG server
  2. convert the KO number downloaded into GI number
  3. then use the blast+ 's gilist function to Blast the GI numbers that I downloaded.

But MY PROBLEM is: I dont know how to do the step 1 and step 2, could anyone provide some procedure to do that? Many thanks,

Kylie

blast kegg identifiers
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updated by jackuser1979 jackuser1979 • written by Shuixia100 • Shuixia100

I think that this question is not sufficiently answered, bumping. Maybe there is a way of doing this by means of blastdbcmd and extracting identifiers? While it might be useful to be able to restrict the search to a certain pathway, it might be useful to be able to extract the complete KEGG portion of NR.

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written by Michael Dondrup Michael Dondrup

2 answers

I think that the references are helpful, however they do not serve as a complete answer but only go half the way. The posts all work for individual ids, but none of them shows a complete example of how to get all GIs which are derived from kegg or have an assigned EC number.

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written by Michael Dondrup Michael Dondrup

I have not tried myself, but there is a bioconductor package called KEGGREST

http://bioconductor.org/packages/release/bioc/html/KEGGREST.html

Here you will find how to retrieve genes from specific pathway

http://grokbase.com/t/r/bioconductor/131xffyqg7/bioc-kegg-rest-retrieving-genes

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written by jackuser1979 jackuser1979

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